Fragment Searching for Bioisosteric Replacement

BROOD is an application designed to aid modelers and medicinal chemists in the selection of possible bioisosteres. Bioisosteric replacement has been a common technique that medicinal chemists have used on a daily basis for decades. BROOD searches a database of pre-generated chemical fragments at a rate of over 100 per second to identify molecular fragments with useful similarities to a query fragment. These fragments are identified by shape, chemistry, electrostatics and/or the geometry of attachment points.

BROOD fragment searching has multiple applications, including lead-hopping, patent breaking, property manipulation, and patent protection by SAR expansion.

Comparison of an ester fragment and an oxazole fragment showing the electrostatic isopotential contour
surfaces. The electrostatic tanimoto between the two fragments is 0.54.

Features

• Identifies from among a database of molecular fragments both obvious and novel replacements of a query fragment
• Packaged with a ready-to-search fragment database of more than 500,000 fragments
• Packaged with a fragmentation utility allowing users to build their own fragment databases
• Allows 1D, 2D or 3D query input, with conformer generation and charging performed on the fly
• Builds whole-molecule analogs of the query molecule based on bioisostere replacement
• Generates 3D overlay of each putative bioisosteric pair
• Searches more than 250,000 fragments per hour
• Provides an output ready to be imported into a spreadsheet

For BROOD and All OpenEye Products

• Multiple file format handling: robust reading and specification-compliant writing of: SMILES, SLN, SDF, MOL, MOL2, PDB, FASTA, MOPAC, MacroModel, XYZ, CCP4, XPLOR, and OEBinary.
• Platform independence: support for Linux, Windows, Mac OS X and many flavors of Unix in both 32 and 64 bit.

<Back to top>